Appeal No. 2002-0796 Page 12
Application No. 09/110,994
Appellants’ arguments that Sparks and Ivanenkov describe protein-protein
interactions, while the Petrenko reference relates to protein-ligand interactions,
are also not convincing. Petrenko, Ivanenkov and Sparks all relate to the ability
to determine a peptide sequence that specifically binds to a binding partner
through the use of a phage display library. One of ordinary skill would expect
that if there were to be difficulties, such difficulties would occur in the screening
of the phage display library to determine the consensus peptide sequence, and
not in using that consensus peptide sequence to search a sequence databank
such as GenBank. Again, as noted, one of ordinary skill would have been
motivated to perform such a searching step using a small consensus sequence
such as that taught by Petrenko in order to determine potential biological targets
and potential unexpected sources of interaction and/or toxicities. Moreover, the
method of claim 1 is not limited to finding natural protein targets of biologically
active small molecules, but to any protein that may contain the consensus
sequence, and thus serve as a source of potential interaction or toxicity.
With respect to Appellants’ argument that the amino acids which form the
binding sites for small ligands must often be presented as a “scaffold,” and one of
ordinary skill in the art would have no reason to expect that “a peptide library
could sufficiently present binding site amino acids in the correct scaffold,” which
appellants assert that they have demonstrated that such correct presentation
does occur. Again, the method of claim 1 is not limited to finding natural protein
targets of biologically active small molecules, but to any protein that may contain
the consensus sequence, and thus serve as a source of potential interaction or
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